Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010647.1 Corchorus capsularis cultivar CVL-1 contig10668, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 26342
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Found at i:2699 original size:30 final size:30
Alignment explanation
Indices: 2597--2699 Score: 109
Period size: 30 Copynumber: 3.4 Consensus size: 30
2587 TCGGTGTTAT
* * *
2597 CATCTTTGGTGTCGTCACCTTTGGTACCAC
1 CATCTTGGGTGCCGTCACCTTTGGTGCCAC
* * *
2627 CATCTTGGGTGCTGTCA-ATTTCGGTGCCAT
1 CATCTTGGGTGCCGTCACCTTT-GGTGCCAC
* * *
2657 CACCTTGAGTGCCGTCACCTTTGGTGTCAC
1 CATCTTGGGTGCCGTCACCTTTGGTGCCAC
2687 CATCTTGGGTGCC
1 CATCTTGGGTGCC
2700 ATCATCTTCG
Statistics
Matches: 57, Mismatches: 14, Indels: 4
0.76 0.19 0.05
Matches are distributed among these distances:
29 3 0.05
30 51 0.89
31 3 0.05
ACGTcount: A:0.13, C:0.29, G:0.24, T:0.34
Consensus pattern (30 bp):
CATCTTGGGTGCCGTCACCTTTGGTGCCAC
Found at i:2705 original size:15 final size:15
Alignment explanation
Indices: 2595--2707 Score: 57
Period size: 15 Copynumber: 7.5 Consensus size: 15
2585 TTTCGGTGTT
* *
2595 ATCATCTTTGGTGTC
1 ATCATCTTGGGTGCC
* * * *
2610 GTCACCTTTGGTACC
1 ATCATCTTGGGTGCC
* *
2625 ACCATCTTGGGTGCT
1 ATCATCTTGGGTGCC
* *
2640 GTCAAT-TTCGGTGCC
1 ATC-ATCTTGGGTGCC
* *
2655 ATCACCTTGAGTGCC
1 ATCATCTTGGGTGCC
* * * *
2670 GTCACCTTTGGTGTC
1 ATCATCTTGGGTGCC
*
2685 ACCATCTTGGGTGCC
1 ATCATCTTGGGTGCC
2700 ATCATCTT
1 ATCATCTT
2708 CGTCCATGAA
Statistics
Matches: 68, Mismatches: 28, Indels: 4
0.68 0.28 0.04
Matches are distributed among these distances:
14 1 0.01
15 65 0.96
16 2 0.03
ACGTcount: A:0.14, C:0.28, G:0.22, T:0.35
Consensus pattern (15 bp):
ATCATCTTGGGTGCC
Found at i:4015 original size:18 final size:18
Alignment explanation
Indices: 3933--4015 Score: 103
Period size: 18 Copynumber: 4.6 Consensus size: 18
3923 AAGTGTGGCA
*
3933 ACTTGGTGCGGTGCGACC
1 ACTTGGTGTGGTGCGACC
*
3951 ACTTGGTGTGGTGCGGCC
1 ACTTGGTGTGGTGCGACC
* * *
3969 ACTAGGTGCGTTGCGACC
1 ACTTGGTGTGGTGCGACC
* *
3987 ATTTGGGGTGGTGCGACC
1 ACTTGGTGTGGTGCGACC
4005 ACTTGGTGTGG
1 ACTTGGTGTGG
4016 CACCATGTGC
Statistics
Matches: 52, Mismatches: 13, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 52 1.00
ACGTcount: A:0.11, C:0.22, G:0.41, T:0.27
Consensus pattern (18 bp):
ACTTGGTGTGGTGCGACC
Found at i:9300 original size:27 final size:27
Alignment explanation
Indices: 9269--9332 Score: 110
Period size: 27 Copynumber: 2.3 Consensus size: 27
9259 ATTTCTGGAA
*
9269 AACAAGGGAAAGGGACAATTAAAAAGG
1 AACAAGGGAAAGAGACAATTAAAAAGG
9296 AACAAGGGAAAGAGACAATTAAAAAGG
1 AACAAGGGAAAGAGACAATTAAAAAGG
9323 AACAGAGGGA
1 AACA-AGGGA
9333 GTATTATCTT
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
27 30 0.86
28 5 0.14
ACGTcount: A:0.56, C:0.08, G:0.30, T:0.06
Consensus pattern (27 bp):
AACAAGGGAAAGAGACAATTAAAAAGG
Found at i:9535 original size:2 final size:2
Alignment explanation
Indices: 9528--9553 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
9518 ATATGTAGTG
9528 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
9554 AACTAATTCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:9690 original size:2 final size:2
Alignment explanation
Indices: 9683--9753 Score: 55
Period size: 2 Copynumber: 37.5 Consensus size: 2
9673 CGAATTCATT
*
9683 TA TA TA TA -A TA -A TA TA -A TA TA TA TA TA TA TA TA AA CTA -A
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA
* *
9722 T- TT TCA TT TA TA TA T- TA TA TA TA TA TA TA TA T
1 TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA T
9754 TCAATTAAAA
Statistics
Matches: 56, Mismatches: 5, Indels: 16
0.73 0.06 0.21
Matches are distributed among these distances:
1 6 0.11
2 48 0.86
3 2 0.04
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:9705 original size:17 final size:17
Alignment explanation
Indices: 9683--9753 Score: 55
Period size: 15 Copynumber: 4.4 Consensus size: 17
9673 CGAATTCATT
9683 TATATATAATA-ATATA
1 TATATATAATATATATA
9699 -ATATAT-ATATATATA
1 TATATATAATATATATA
* *
9714 TA-A-ACTAAT-TTTCATT
1 TATATA-TAATATAT-ATA
*
9730 TATATATTATATATATA
1 TATATATAATATATATA
9747 TATATAT
1 TATATAT
9754 TCAATTAAAA
Statistics
Matches: 42, Mismatches: 5, Indels: 15
0.68 0.08 0.24
Matches are distributed among these distances:
14 4 0.10
15 15 0.36
16 7 0.17
17 13 0.31
18 3 0.07
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.49
Consensus pattern (17 bp):
TATATATAATATATATA
Found at i:10188 original size:44 final size:45
Alignment explanation
Indices: 10139--10227 Score: 162
Period size: 45 Copynumber: 2.0 Consensus size: 45
10129 GATTACTTCT
*
10139 CCAGCTCATCATTAA-TCTGGGTAGGGATCTTTTAGTAATTCCAC
1 CCAGCTCATCATTAATTCGGGGTAGGGATCTTTTAGTAATTCCAC
10183 CCAGCTCATCATTAATTCGGGGTAGGGATCTTTTAGTAATTCCAC
1 CCAGCTCATCATTAATTCGGGGTAGGGATCTTTTAGTAATTCCAC
10228 TACTCTATTA
Statistics
Matches: 43, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
44 15 0.35
45 28 0.65
ACGTcount: A:0.25, C:0.22, G:0.19, T:0.34
Consensus pattern (45 bp):
CCAGCTCATCATTAATTCGGGGTAGGGATCTTTTAGTAATTCCAC
Found at i:13841 original size:33 final size:32
Alignment explanation
Indices: 13723--13843 Score: 147
Period size: 33 Copynumber: 3.8 Consensus size: 32
13713 TCTCTTTCTC
* * *
13723 GTCACCCAAAACAGATTTATTTTCAATGCCA-
1 GTCAACCAAAACAGAATTATTTTCAATGCTAT
* *
13754 -TCAACCAAAACAGGATTATTTGCAATGCTAT
1 GTCAACCAAAACAGAATTATTTTCAATGCTAT
* *
13785 GATCAACCAAAACAAAATTATTTTTAATGCTAT
1 G-TCAACCAAAACAGAATTATTTTCAATGCTAT
13818 GTTCAACCAAAACAGAATTATTTTCA
1 G-TCAACCAAAACAGAATTATTTTCA
13844 TCACAATTAG
Statistics
Matches: 75, Mismatches: 12, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
30 25 0.33
33 50 0.67
ACGTcount: A:0.40, C:0.20, G:0.09, T:0.31
Consensus pattern (32 bp):
GTCAACCAAAACAGAATTATTTTCAATGCTAT
Found at i:17830 original size:12 final size:11
Alignment explanation
Indices: 17810--17839 Score: 51
Period size: 12 Copynumber: 2.6 Consensus size: 11
17800 GGAAAATATC
17810 AAAAAATAAAT
1 AAAAAATAAAT
17821 AAATAAATAAAT
1 AAA-AAATAAAT
17833 AAAAAAT
1 AAAAAAT
17840 TTCGATCAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 7 0.39
12 11 0.61
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (11 bp):
AAAAAATAAAT
Found at i:19127 original size:53 final size:53
Alignment explanation
Indices: 19031--19237 Score: 290
Period size: 53 Copynumber: 3.9 Consensus size: 53
19021 CATTTATAAG
* * *
19031 TCCCTAAACACAGAGGCAATTCTATATCAAAAGACCTCGAACACAAGGGTGTTCA
1 TCCCTAAACACAGAGGC-A-TCTATATCAAAAGTCCTCAAACACAAGGGTATTCA
*
19086 TCCCTAAACATAGAGGCATCTATATCAAAAGTCCTCAAACACAAGGGTATTCA
1 TCCCTAAACACAGAGGCATCTATATCAAAAGTCCTCAAACACAAGGGTATTCA
* * * *
19139 TCCCTAAACACAAAGGCACCTCTCTCAAAAGTCCTCAAACACAAGGGTATTCA
1 TCCCTAAACACAGAGGCATCTATATCAAAAGTCCTCAAACACAAGGGTATTCA
* * *
19192 TCCCTAAACACAGAGGCATCTACATC-AAAGTCTTCAAGCACAAGGG
1 TCCCTAAACACAGAGGCATCTATATCAAAAGTCCTCAAACACAAGGG
19238 CATCCATACT
Statistics
Matches: 136, Mismatches: 16, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
52 18 0.13
53 101 0.74
54 1 0.01
55 16 0.12
ACGTcount: A:0.38, C:0.28, G:0.14, T:0.20
Consensus pattern (53 bp):
TCCCTAAACACAGAGGCATCTATATCAAAAGTCCTCAAACACAAGGGTATTCA
Found at i:19252 original size:30 final size:30
Alignment explanation
Indices: 19192--19285 Score: 97
Period size: 30 Copynumber: 3.1 Consensus size: 30
19182 AGGGTATTCA
19192 TCCCTAAACACAGAGGCAT-C-TACATCAAAG
1 TCCCTAAACACAGAGGCATCCATAC-T-AAAG
* *
19222 T-CTTCAAGCACA-AGGGCATCCATACTAAAG
1 TCCCT-AAACACAGA-GGCATCCATACTAAAG
*
19252 TCCCTAAACACAGAGGCATCTATACTAAAG
1 TCCCTAAACACAGAGGCATCCATACTAAAG
19282 TCCC
1 TCCC
19286 CAAATACATG
Statistics
Matches: 53, Mismatches: 5, Indels: 12
0.76 0.07 0.17
Matches are distributed among these distances:
29 3 0.06
30 42 0.79
31 5 0.09
32 3 0.06
ACGTcount: A:0.37, C:0.30, G:0.14, T:0.19
Consensus pattern (30 bp):
TCCCTAAACACAGAGGCATCCATACTAAAG
Found at i:25838 original size:19 final size:18
Alignment explanation
Indices: 25805--25840 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
25795 TTGAAATAAT
25805 TCTTCAATGATCTTCAAA
1 TCTTCAATGATCTTCAAA
*
25823 TCTTCAAATTATCTTCAA
1 TCTTC-AATGATCTTCAA
25841 GAAATCTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.33, C:0.22, G:0.03, T:0.42
Consensus pattern (18 bp):
TCTTCAATGATCTTCAAA
Done.